1
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Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R. Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression. bioRxiv 2024:2024.03.19.585820. [PMID: 38562901 PMCID: PMC10983923 DOI: 10.1101/2024.03.19.585820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive disorder (MDD), as defined by DSM-IV or V criteria. The study also examined the influence of medication use, particularly antidepressants and/or anxiolytics, classified through the Anatomical Therapeutic Chemical (ATC) Classification System, on the gut microbiota. Both 16S rRNA gene amplicon sequencing and shallow shotgun sequencing were performed on DNA extracted from 666 fecal samples from the Tulsa-1000 and NeuroMAP CoBRE cohorts. The results highlight the significant influence of medication use; antidepressant use is associated with significant differences in gut microbiota beta diversity and has a larger effect size than NPD diagnosis. Next, specific microbes were associated with ANXD and MDD, highlighting their potential for non-pharmacological intervention. Finally, the study demonstrated the capability of Random Forest classifiers to predict diagnoses of NPD and medication use from microbial profiles, suggesting a promising direction for the use of gut microbiota as biomarkers for NPD. The findings suggest that future research on the gut microbiota's role in NPD and its interactions with pharmacological treatments are needed.
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Affiliation(s)
- Amanda Hazel Dilmore
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Rayus Kuplicki
- Laureate Institute for Brain Research, Tulsa, Oklahoma, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Megha Kumar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Alexander Tyakht
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colette Blach
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Boadie W. Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Sudeepa Bhattacharyya
- Department of Biological Sciences, Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, USA
| | | | - Pooja Mandaviya
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Rima Kaddaruh-Dauok
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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2
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Burcham ZM, Belk AD, McGivern BB, Bouslimani A, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel HL, Xu ZZ, Nieciecki V, Zhu Q, Shaffer M, Panitchpakdi M, Weldon KC, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Chan SHJ, Connor M, Boyd D, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Dorrestein PC, Wrighton KC, Carter DO, Knight R, Metcalf JL. A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nat Microbiol 2024; 9:595-613. [PMID: 38347104 PMCID: PMC10914610 DOI: 10.1038/s41564-023-01580-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/08/2023] [Indexed: 03/07/2024]
Abstract
Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.
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Affiliation(s)
- Zachary M Burcham
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Aeriel D Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Animal Sciences, Auburn University, Auburn, AL, USA
| | - Bridget B McGivern
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Parsa Ghadermazi
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
- Institute for Systems Genetics, New York Grossman School of Medicine, New York University, New York, NY, USA
- Department of Computer Science, New York University, New York, NY, USA
| | - Anru R Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Pixu Shi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Alexandra Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Heather L Deel
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhenjiang Zech Xu
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Victoria Nieciecki
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Greg C Humphry
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Siu Hung Joshua Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Melissa Connor
- Forensic Investigation Research Station, Colorado Mesa University, Grand Junction, CO, USA
| | - Derek Boyd
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Department of Social, Cultural, and Justice Studies, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Jake Smith
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Mid-America College of Funeral Service, Jeffersonville, IN, USA
| | - Jenna M S Watson
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Giovanna Vidoli
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Dawnie Steadman
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Aaron M Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
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3
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Vänni P, Tejesvi MV, Paalanne N, Aagaard K, Ackermann G, Camargo CA, Eggesbø M, Hasegawa K, Hoen AG, Karagas MR, Kolho KL, Laursen MF, Ludvigsson J, Madan J, Ownby D, Stanton C, Stokholm J, Tapiainen T. Machine-learning analysis of cross-study samples according to the gut microbiome in 12 infant cohorts. mSystems 2023; 8:e0036423. [PMID: 37874156 PMCID: PMC10734493 DOI: 10.1128/msystems.00364-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/13/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE There are challenges in merging microbiome data from diverse research groups due to the intricate and multifaceted nature of such data. To address this, we utilized a combination of machine-learning (ML) models to analyze 16S sequencing data from a substantial set of gut microbiome samples, sourced from 12 distinct infant cohorts that were gathered prospectively. Our initial focus was on the mode of delivery due to its prior association with changes in infant gut microbiomes. Through ML analysis, we demonstrated the effective merging and comparison of various gut microbiome data sets, facilitating the identification of robust microbiome biomarkers applicable across varied study populations.
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Affiliation(s)
- Petri Vänni
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Mysore V. Tejesvi
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Kjersti Aagaard
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Merete Eggesbø
- Department of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Kaija-Leena Kolho
- Children’s Hospital, University of Helsinki and HUS, Helsinki, Finland
| | - Martin F. Laursen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Johnny Ludvigsson
- Crown Princess Victoria Children’s Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Juliette Madan
- Department of Psychiatry, Dartmouth Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Department of Pediatrics, Dartmouth Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Dennis Ownby
- Medical College of Georgia, Augusta, Georgia, USA
| | - Catherine Stanton
- Teagasc Food Research Centre & APC Microbiome Ireland, Moorepark, Fermoy, Co. Cork, Ireland
| | - Jakob Stokholm
- Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
- Biocenter Oulu, University of Oulu, Oulu, Finland
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4
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Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 2023; 41:1656. [PMID: 37853256 DOI: 10.1038/s41587-023-02025-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kiana A West
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Candace L Williams
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole C Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edgar Diaz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kate E Sprecher
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniela Vargas-Robles
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela
| | - Dana Withrow
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, MT, USA
| | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lucas Maciel Mauriz Marques
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Juliano Geraldo Amaral
- Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Rodrigo Moreira Silva
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Flavio Protasio Veras
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Rene Donizeti Ribeiro Oliveira
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Paulo Louzada-Junior
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Robert H Mills
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Paulina K Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Rima Kaddurah Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Curt Wittenberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Terkeltaub
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- San Diego VA Healthcare System, San Diego, CA, USA
| | - Megan M Doty
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Jae H Kim
- Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kyung E Rhee
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julia Beauchamp-Walters
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mark Manary
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Monica Guma
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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5
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Pendergraft MA, Belda-Ferre P, Petras D, Morris CK, Mitts BA, Aron AT, Bryant M, Schwartz T, Ackermann G, Humphrey G, Kaandorp E, Dorrestein PC, Knight R, Prather KA. Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol. Environ Sci Technol 2023; 57:4071-4081. [PMID: 36862087 PMCID: PMC10018732 DOI: 10.1021/acs.est.2c02312] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Roughly half of the human population lives near the coast, and coastal water pollution (CWP) is widespread. Coastal waters along Tijuana, Mexico, and Imperial Beach (IB), USA, are frequently polluted by millions of gallons of untreated sewage and stormwater runoff. Entering coastal waters causes over 100 million global annual illnesses, but CWP has the potential to reach many more people on land via transfer in sea spray aerosol (SSA). Using 16S rRNA gene amplicon sequencing, we found sewage-associated bacteria in the polluted Tijuana River flowing into coastal waters and returning to land in marine aerosol. Tentative chemical identification from non-targeted tandem mass spectrometry identified anthropogenic compounds as chemical indicators of aerosolized CWP, but they were ubiquitous and present at highest concentrations in continental aerosol. Bacteria were better tracers of airborne CWP, and 40 tracer bacteria comprised up to 76% of the bacteria community in IB air. These findings confirm that CWP transfers in SSA and exposes many people along the coast. Climate change may exacerbate CWP with more extreme storms, and our findings call for minimizing CWP and investigating the health effects of airborne exposure.
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Affiliation(s)
- Matthew A. Pendergraft
- Scripps
Institution of Oceanography, University
of California San Diego, San Diego, La Jolla, California 92037, United States
| | - Pedro Belda-Ferre
- Department
of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
| | - Daniel Petras
- Scripps
Institution of Oceanography, University
of California San Diego, San Diego, La Jolla, California 92037, United States
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Science, University of California, San Diego, La Jolla, California 92093, United States
- CMFI
Cluster of Excellence, Interfaculty Institute of Microbiology and
Medicine, University of Tuebingen, Tuebingen 72076, Germany
| | - Clare K. Morris
- Scripps
Institution of Oceanography, University
of California San Diego, San Diego, La Jolla, California 92037, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Brock A. Mitts
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Allegra T. Aron
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Science, University of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United
States
| | - MacKenzie Bryant
- Department
of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
| | - Tara Schwartz
- Department
of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
| | - Gail Ackermann
- Department
of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
| | - Greg Humphrey
- Department
of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
| | - Ethan Kaandorp
- Independent
Researcher, Darwin, California 93522, United States
| | - Pieter C. Dorrestein
- Department
of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Science, University of California, San Diego, La Jolla, California 92093, United States
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093, United States
| | - Rob Knight
- Department
of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093, United States
- Department
of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Department
of Computer Sciences and Engineering, University
of California, San Diego, La Jolla, California 92093, United States
| | - Kimberly A. Prather
- Scripps
Institution of Oceanography, University
of California San Diego, San Diego, La Jolla, California 92037, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
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6
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Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A, Mazmanian SK. Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome. Mov Disord 2023; 38:399-409. [PMID: 36691982 DOI: 10.1002/mds.29300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD). OBJECTIVES The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression. METHODS Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features. RESULTS We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling. CONCLUSIONS A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Joseph C Boktor
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Gil Sharon
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Leo A Verhagen Metman
- Department of Neurology Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Deborah A Hall
- Department of Neurology Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Zoe Zreloff
- The BioCollective, LLC, Denver, Colorado, USA
| | - Daniel J Hakim
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - John W Bostick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - James Ousey
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | - Gregory Humphrey
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
- Departments of Internal Medicine, Anatomy & Cell Biology, Rush University Medical Center, Chicago, Illinois, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
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7
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Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 2022; 40:1774-1779. [PMID: 35798960 PMCID: PMC10277029 DOI: 10.1038/s41587-022-01368-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 05/20/2022] [Indexed: 01/30/2023]
Abstract
Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.
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Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kiana A West
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Candace L Williams
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole C Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edgar Diaz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kate E Sprecher
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniela Vargas-Robles
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela
| | - Dana Withrow
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, MT, USA
| | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lucas Maciel Mauriz Marques
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Juliano Geraldo Amaral
- Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Rodrigo Moreira Silva
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Flavio Protasio Veras
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Rene Donizeti Ribeiro Oliveira
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Paulo Louzada-Junior
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Robert H Mills
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Paulina K Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Rima Kaddurah Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Curt Wittenberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Terkeltaub
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- San Diego VA Healthcare System, San Diego, CA, USA
| | - Megan M Doty
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Jae H Kim
- Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kyung E Rhee
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julia Beauchamp-Walters
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mark Manary
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Monica Guma
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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8
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Zhou X, Baumann R, Gao X, Mendoza M, Singh S, Sand IK, Xia Z, Cox LM, Chitnis T, Yoon H, Moles L, Caillier SJ, Santaniello A, Ackermann G, Harroud A, Lincoln R, Gomez R, Peña AG, Digga E, Hakim DJ, Vazquez-Baeza Y, Soman K, Warto S, Humphrey G, Farez M, Gerdes LA, Oksenberg JR, Zamvil SS, Chandran S, Connick P, Otaegui D, Castillo-Triviño T, Hauser SL, Gelfand JM, Weiner HL, Hohlfeld R, Wekerle H, Graves J, Bar-Or A, Cree BA, Correale J, Knight R, Baranzini SE. Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course. Cell 2022; 185:3467-3486.e16. [PMID: 36113426 PMCID: PMC10143502 DOI: 10.1016/j.cell.2022.08.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 04/21/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
Changes in gut microbiota have been associated with several diseases. Here, the International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of 576 MS patients (36% untreated) and genetically unrelated household healthy controls (1,152 total subjects). We observed a significantly increased proportion of Akkermansia muciniphila, Ruthenibacterium lactatiformans, Hungatella hathewayi, and Eisenbergiella tayi and decreased Faecalibacterium prausnitzii and Blautia species. The phytate degradation pathway was over-represented in untreated MS, while pyruvate-producing carbohydrate metabolism pathways were significantly reduced. Microbiome composition, function, and derived metabolites also differed in response to disease-modifying treatments. The therapeutic activity of interferon-β may in part be associated with upregulation of short-chain fatty acid transporters. Distinct microbial networks were observed in untreated MS and healthy controls. These results strongly support specific gut microbiome associations with MS risk, course and progression, and functional changes in response to treatment.
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Affiliation(s)
- Xiaoyuan Zhou
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Ryan Baumann
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Xiaohui Gao
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Myra Mendoza
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Sneha Singh
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Ilana Katz Sand
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lau M. Cox
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tanuja Chitnis
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hongsup Yoon
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospitals, Ludwig-Maximilians-Universität München, and Munich Cluster of Systems Neurology (SyNergy), München, Germany
- Department Neuroimmunology, Max Planck Institute (MPI) of Neurobiology, Munich, Germany
| | - Laura Moles
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Stacy J. Caillier
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Adam Santaniello
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Adil Harroud
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Robin Lincoln
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | | | | | - Elise Digga
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Joseph Hakim
- Department of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA
| | - Yoshiki Vazquez-Baeza
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Karthik Soman
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Shannon Warto
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Mauricio Farez
- Department of Neurology, Institute for Neurological Research Dr. Raul Carrea (FLENI), Buenos Aires, Argentina
| | - Lisa Ann Gerdes
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Scott S. Zamvil
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | | | - Peter Connick
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - David Otaegui
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Tamara Castillo-Triviño
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
- Department of Neurology, Hospital Universitario Donostia and Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Stephen L. Hauser
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Jeffrey M. Gelfand
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Howard L. Weiner
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospitals, Ludwig-Maximilians-Universität München, and Munich Cluster of Systems Neurology (SyNergy), München, Germany
| | - Hartmut Wekerle
- Department Neuroimmunology, Max Planck Institute (MPI) of Neurobiology, Munich, Germany
| | - Jennifer Graves
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Amit Bar-Or
- Department of Neurology, University of Pennsylvania, Pennsylvania, PA, USA
| | - Bruce A.C. Cree
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Jorge Correale
- Department of Neurology, Institute for Neurological Research Dr. Raul Carrea (FLENI), Buenos Aires, Argentina
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Sergio E. Baranzini
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
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9
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Gonzalez CG, Mills RH, Kordahi MC, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey JC, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients. Cell Mol Gastroenterol Hepatol 2022; 14:35-53. [PMID: 35378331 PMCID: PMC9117812 DOI: 10.1016/j.jcmgh.2022.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. METHODS Pre- and post-intervention mucosal biopsies, tissue, and fecal samples were collected from HBOT phase 2 clinical trials. Biopsies and fecal samples were subjected to shotgun metaproteomics, metabolomics, 16s rRNA sequencing, and metagenomics. Tissue was subjected to bulk RNA sequencing and digital spatial profiling (DSP) for single-cell RNA and protein analysis, and immunohistochemistry was performed. Fecal samples were also used for colonization experiments in IL10-/- germ-free UC mouse models. RESULTS Proteomics identified negative associations between HBOT response and neutrophil azurophilic granule abundance. DSP identified an HBOT-specific reduction of neutrophil STAT3, which was confirmed by immunohistochemistry. HBOT decreased microbial diversity with a proportional increase in Firmicutes and a secondary bile acid lithocholic acid. A major source of the reduction in diversity was the loss of mucus-adherent taxa, resulting in increased MUC2 levels post-HBOT. Targeted database searching revealed strain-level associations between Akkermansia muciniphila and HBOT response status. Colonization of IL10-/- with stool obtained from HBOT responders resulted in lower colitis activity compared with non-responders, with no differences in STAT3 expression, suggesting complementary but independent host and microbial responses. CONCLUSIONS HBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients and changes in microbial composition and metabolism in ways that improve colitis activity. Intestinal microbiota, especially strain level variations in A muciniphila, may contribute to HBOT non-response.
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Key Words
- bclxl, b-cell lymphoma-extra large
- bim, bcl-2 interacting protein
- dsp, digital spatial profiling
- fdr, false discovery rate
- hbot, hyperbaric oxygen therapy
- hif, hypoxia inducible factor
- il, interleukin
- lca, lithocholic acid
- mapk, mitogen-activated protein kinase
- ms, mass spectrometry
- nlrp3, nod-, lrr- and pyrin domain-containing protein 3
- roi, regions of interest
- ros, reactive oxygen species
- stat3, signal transducer and activator of transcription 3
- tmt, tandem mass tag
- uc, ulcerative colitis
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Affiliation(s)
- Carlos G. Gonzalez
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Pediatrics, University of California, San Diego, California
| | - Robert H. Mills
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Pediatrics, University of California, San Diego, California
| | - Melissa C. Kordahi
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université de Paris, Paris, France
| | - Marvic Carrillo-Terrazas
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California
| | - Henry Secaira-Morocho
- School of Life Sciences, Arizona State University, Tempe, Arizona,Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona
| | - Christella E. Widjaja
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Matthew S. Tsai
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Yash Mittal
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California,Institute for Genomic Medicine, University of California San Diego, San Diego, California
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California
| | - Kelly Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Computer Science and Engineering, University of California San Diego, San Diego, California
| | - Julia M. Gauglitz
- Department of Pediatrics, University of California, San Diego, California
| | - Clara Delaroque
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université de Paris, Paris, France
| | - Consuelo Sauceda
- Department of Pharmacology, University of California, San Diego, California
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, California
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, California
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, California
| | - Austin D. Swafford
- Department of Computer Science and Engineering, University of California San Diego, San Diego, California
| | - Corey A. Siegel
- Section of Gastroenterology and Hepatology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Jay C. Buckey
- Center for Hyperbaric Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Laura E. Raffals
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Charlotte Sadler
- Division of Hyperbaric Medicine, Department of Emergency Medicine, University of California San Diego, San Diego, California
| | - Peter Lindholm
- Division of Hyperbaric Medicine, Department of Emergency Medicine, University of California San Diego, San Diego, California
| | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, San Diego, California
| | - Mark Valaseck
- Department of Pathology, University of California San Diego, San Diego, California
| | - Arief Suriawinata
- Section of Gastroenterology and Hepatology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California,Institute for Genomic Medicine, University of California San Diego, San Diego, California
| | - Pradipta Ghosh
- Division of Gastroenterology, University of California San Diego, San Diego, California,Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California
| | - John T. Chang
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Hiutung Chu
- Department of Pathology, University of California San Diego, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California,Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, California
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Pediatrics, University of California, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, Arizona,Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona
| | - Benoit Chassaing
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université de Paris, Paris, France
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, California,Department of Pediatrics, University of California, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California
| | - Parambir S. Dulai
- Division of Gastroenterology, University of California San Diego, San Diego, California,Division of Gastroenterology, Northwestern University, Chicago, Illinois,Correspondence Address correspondence to: Parambir S. Dulai, MD, Division of Gastroenterology & Hepatology, Northwestern University Feinberg School of Medicine, Arkes Pavilion, 676 North St Clair Street, 14th Floor, Chicago, Illinois 60611. fax: (858) 657-5022.
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10
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Kosciolek T, Victor TA, Kuplicki R, Rossi M, Estaki M, Ackermann G, Knight R, Paulus MP. Individuals with substance use disorders have a distinct oral microbiome pattern. Brain Behav Immun Health 2021; 15:100271. [PMID: 34589776 PMCID: PMC8474247 DOI: 10.1016/j.bbih.2021.100271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/22/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022] Open
Abstract
Background Substance use disorder emerges from a complex interaction between genetic predisposition, life experiences, exposure, and subsequent adaptation of biological systems to the repeated use of drugs. Recently, investigators have proposed that the human microbiota may play a role in brain health and disease. In particular, the human oral microbiome is a distinct and diverse ecological niche with its composition influenced by external factors such as lifestyle, diet, and oral hygiene. This investigation examined whether individuals with substance use disorder (SU) show a different oral microbiome pattern and whether this pattern is sufficient to delineate the SU group from healthy comparison (HC) subjects. Methods Participants were a sub-sample (N = 177) of the Tulsa 1000 (T-1000) project. We analyzed 123 SU and 54 HC subjects using 16S rRNA marker gene sequencing to characterize the oral microbiome. Results The groups differed significantly based on the UniFrac distance, a phylogenetic-based measure of beta diversity, but did not differ in alpha diversity. Using a machine learning approach, microbiome features combined with socio-demographic variables successfully categorized group membership with 87%–92% accuracy, even after controlling for external factors such as smoking or alcohol consumption. SU individuals with relatively lower diversity also reported higher levels of negative reinforcement experiences associated with their primary substance of abuse. Conclusions Oral microbiome features are useful to sufficiently differentiate SU from HC subjects. There is some evidence that subjects whose drug use is driven by negative reinforcement show an impoverished oral microbiome. Taken together, the oral microbiome may help to understand the dysfunctional biological processes that promote substance use or may be pragmatically useful as a risk or severity biological marker. Oral microbiome features differentiate substance use disorder and healthy subjects. Machine learning with microbiome and socio-demographic variables categorizes groups. Substance use individuals have lower microbiome diversity. Substance use individuals have higher levels of negative reinforcement. Oral microbiome may be useful as a risk or severity biological marker.
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Affiliation(s)
- Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | | | | | - Maret Rossi
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, CA, USA.,Department of Bioengineering, University of California San Diego, CA, USA
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11
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome 2021; 9:132. [PMID: 34103074 PMCID: PMC8186369 DOI: 10.1186/s40168-021-01083-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. METHODS We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. RESULTS Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. CONCLUSIONS These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment. Video Abstract.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mac Kenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | | | - Laxmi Parida
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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12
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Fang X, Vázquez-Baeza Y, Elijah E, Vargas F, Ackermann G, Humphrey G, Lau R, Weldon KC, Sanders JG, Panitchpakdi M, Carpenter C, Jarmusch AK, Neill J, Miralles A, Dulai P, Singh S, Tsai M, Swafford AD, Smarr L, Boyle DL, Palsson BO, Chang JT, Dorrestein PC, Sandborn WJ, Knight R, Boland BS. Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. Inflamm Bowel Dis 2021; 27:603-616. [PMID: 33026068 PMCID: PMC8047854 DOI: 10.1093/ibd/izaa262] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Many studies have investigated the role of the microbiome in inflammatory bowel disease (IBD), but few have focused on surgery specifically or its consequences on the metabolome that may differ by surgery type and require longitudinal sampling. Our objective was to characterize and contrast microbiome and metabolome changes after different surgeries for IBD, including ileocolonic resection and colectomy. METHODS The UC San Diego IBD Biobank was used to prospectively collect 332 stool samples from 129 subjects (50 ulcerative colitis; 79 Crohn's disease). Of these, 21 with Crohn's disease had ileocolonic resections, and 17 had colectomies. We used shotgun metagenomics and untargeted liquid chromatography followed by tandem mass spectrometry metabolomics to characterize the microbiomes and metabolomes of these patients up to 24 months after the initial sampling. RESULTS The species diversity and metabolite diversity both differed significantly among groups (species diversity: Mann-Whitney U test P value = 7.8e-17; metabolomics, P-value = 0.0043). Escherichia coli in particular expanded dramatically in relative abundance in subjects undergoing surgery. The species profile was better able to classify subjects according to surgery status than the metabolite profile (average precision 0.80 vs 0.68). CONCLUSIONS Intestinal surgeries seem to reduce the diversity of the gut microbiome and metabolome in IBD patients, and these changes may persist. Surgery also further destabilizes the microbiome (but not the metabolome) over time, even relative to the previously established instability in the microbiome of IBD patients. These long-term effects and their consequences for health outcomes need to be studied in prospective longitudinal trials linked to microbiome-involved phenotypes.
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Affiliation(s)
- Xin Fang
- Department of Bioengineering University of California, San Diego, CA, USA
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering University of California, San Diego, CA, USA
- Center for Microbiome Innovation University of California, San Diego, CA, USA
| | - Emmanuel Elijah
- Center for Microbiome Innovation University of California, San Diego, CA, USA
| | - Fernando Vargas
- Department of Pharmacology University of California, San Diego, CA, USA
| | - Gail Ackermann
- Department of Pediatrics University of California, San Diego, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics University of California, San Diego, CA, USA
| | - Rebecca Lau
- Department of Cellular and Molecular Medicine University of California, San Diego, CA, USA
| | - Kelly C Weldon
- Center for Microbiome Innovation University of California, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, CA, USA
| | - Jon G Sanders
- Department of Bioengineering University of California, San Diego, CA, USA
- Cornell Institute of Host–Microbe Interaction and Disease, Cornell University, Ithaca, NY, USA
| | | | - Carolina Carpenter
- Center for Microbiome Innovation University of California, San Diego, CA, USA
| | - Alan K Jarmusch
- Department of Pharmacology University of California, San Diego, CA, USA
| | - Jennifer Neill
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
| | - Ara Miralles
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
| | - Parambir Dulai
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
| | - Matthew Tsai
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation University of California, San Diego, CA, USA
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
- California Institute for Telecommunications and Information Technology, University of California, San Diego, CA, USA
| | - David L Boyle
- Division of Rheumatology, Department of Medicine, University of California, San Diego, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering University of California, San Diego, CA, USA
- Department of Pediatrics University of California, San Diego, CA, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
| | - Pieter C Dorrestein
- Department of Pharmacology University of California, San Diego, CA, USA
- Department of Pediatrics University of California, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, CA, USA
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
| | - Rob Knight
- Department of Bioengineering University of California, San Diego, CA, USA
- Center for Microbiome Innovation University of California, San Diego, CA, USA
- Department of Pediatrics University of California, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, CA, USA
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13
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Mu A, McDonald D, Jarmusch AK, Martino C, Brennan C, Bryant M, Humphrey GC, Toronczak J, Schwartz T, Nguyen D, Ackermann G, D'Onofrio A, Strathdee SA, Schooley RT, Dorrestein PC, Knight R, Aslam S. Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection. Microbiome 2021; 9:92. [PMID: 33853672 PMCID: PMC8048313 DOI: 10.1186/s40168-021-01026-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/05/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood. RESULTS Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum. CONCLUSION Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections. Video abstract.
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Affiliation(s)
- Andre Mu
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of San Diego, La Jolla, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Mackenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gregory C Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Julia Toronczak
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Dominic Nguyen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Anthony D'Onofrio
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, USA
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Sciences and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
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14
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Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. Biotechniques 2021; 70:149-159. [PMID: 33512248 PMCID: PMC7931620 DOI: 10.2144/btn-2020-0153] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.
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Affiliation(s)
- Justin P Shaffer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics & Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Carolina S Carpenter
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Livia S Zaramela
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, University of California, San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Micronoma Inc., San Diego, CA, USA
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15
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Gruenewald T, Pellissier V, Philipp E, Wolfensteller K, Hoffmann I, Zabel R, Ackermann G, Pöge A, Linde J, Lakowa N. Antimicrobial resistance in Helicobacter pylori – State-wide surveillance from the Saxony antibiotic network project (ABNW). Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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16
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Lakowa N, Pellissier V, Ackermann G, Zabel R, Hoffmann I, Philipp E, Wolfensteller K, Pöge A, Linde J, Gruenewald T. Antimicrobial resistance to rescue substances in Gram-negative ESKAPE pathogens – State-wide surveillance from the Saxony antibiotic network project. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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17
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Thomas RL, Jiang L, Adams JS, Xu ZZ, Shen J, Janssen S, Ackermann G, Vanderschueren D, Pauwels S, Knight R, Orwoll ES, Kado DM. Vitamin D metabolites and the gut microbiome in older men. Nat Commun 2020; 11:5997. [PMID: 33244003 PMCID: PMC7693238 DOI: 10.1038/s41467-020-19793-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
The vitamin D receptor is highly expressed in the gastrointestinal tract where it transacts gene expression. With current limited understanding of the interactions between the gut microbiome and vitamin D, we conduct a cross-sectional analysis of 567 older men quantifying serum vitamin D metabolites using LC-MSMS and defining stool sub-Operational Taxonomic Units from16S ribosomal RNA gene sequencing data. Faith’s Phylogenetic Diversity and non-redundant covariate analyses reveal that the serum 1,25(OH)2D level explains 5% of variance in α-diversity. In β-diversity analyses using unweighted UniFrac, 1,25(OH)2D is the strongest factor assessed, explaining 2% of variance. Random forest analyses identify 12 taxa, 11 in the phylum Firmicutes, eight of which are positively associated with either 1,25(OH)2D and/or the hormone-to-prohormone [1,25(OH)2D/25(OH)D] “activation ratio.” Men with higher levels of 1,25(OH)2D and higher activation ratios, but not 25(OH)D itself, are more likely to possess butyrate producing bacteria that are associated with better gut microbial health. Here, the authors investigate associations of vitamin D metabolites with gut microbiome in a cross-sectional analysis of 567 elderly men enrolled in the Osteoporotic Fractures in Men (MrOS) Study and find larger alpha-diversity correlates with high 1,25(OH)2D and high 24,25(OH)2D and higher ratios of activation and catabolism.
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Affiliation(s)
- Robert L Thomas
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lingjing Jiang
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - John S Adams
- Departments of Orthopaedic Surgery and Molecular, Cell and Developmental Biology at UCLA, Los Angeles, CA, USA
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Jian Shen
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Stefan Janssen
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus-Liebig-University, Gießen, Germany
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Dirk Vanderschueren
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium.,Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Steven Pauwels
- Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, B-3000, Leuven, Belgium.,Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium.,Department of Laboratory Medicine, Jessa Hospital, Hasselt, Belgium
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,UC San Diego Center for Microbiome Innovation, La Jolla, CA, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Eric S Orwoll
- Department of Medicine, Bone and Mineral Unit, Oregon Health & Sciences University, Portland, OR, USA
| | - Deborah M Kado
- Department of Medicine, University of California San Diego, La Jolla, CA, USA. .,Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.
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18
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM. Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment. medRxiv 2020:2020.11.19.20234229. [PMID: 33236030 PMCID: PMC7685343 DOI: 10.1101/2020.11.19.20234229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (COVID-19), their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and contextualized the massive microbial diversity in this dataset in a meta-analysis of over 20,000 samples. Sixteen percent of surfaces from COVID-19 patient rooms were positive, with the highest prevalence in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples increasingly resembled the patient microbiome throughout their stay, SARS-CoV-2 was less frequently detected there (11%). Despite surface contamination in almost all patient rooms, no health care workers providing COVID-19 patient care contracted the disease. SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity across human and surface samples, and higher biomass in floor samples. 16S microbial community profiles allowed for high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia was highly predictive of SARS-CoV-2 across sample types, and had higher prevalence in positive surface and human samples, even when comparing to samples from patients in another intensive care unit prior to the COVID-19 pandemic. These results suggest that bacterial communities contribute to viral prevalence both in the host and hospital environment.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, California, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | | | - Laxmi Parida
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, California, USA
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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19
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Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. bioRxiv 2020:2020.11.13.370387. [PMID: 33200135 PMCID: PMC7668742 DOI: 10.1101/2020.11.13.370387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One goal among microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods we previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, we compare the relative performance of two total nucleic acid extraction protocols and our previously benchmarked protocol. We included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here we present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection, and well-to-well contamination, between these protocols. Accession numbers Raw sequence data were deposited at the European Nucleotide Archive (accession#: ERP124610) and raw and processed data are available at Qiita (Study ID: 12201). All processing and analysis code is available on GitHub ( github.com/justinshaffer/Extraction_test_MagMAX ). Methods summary To allow for downstream applications involving RNA-based organisms such as SARS-CoV-2, we compared the two extraction protocols designed to extract DNA and RNA against our previously established protocol for extracting only DNA for microbial community analyses. Across 10 diverse sample types, one of the two protocols was equivalent or better than our established DNA-based protocol. Our conclusion is based on per-sample comparisons of DNA and RNA yield, the number of quality sequences generated, microbial community alpha- and beta-diversity and taxonomic composition, the limit of detection, and extent of well-to-well contamination.
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20
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Zhou X, Singh S, Baumann R, Barba P, Landefeld J, Casaccia P, Sand IK, Xia Z, Weiner H, Chitnis T, Chandran S, Connick P, Otaegui D, Castillo-Triviño T, Caillier SJ, Santaniello A, Ackermann G, Humphrey G, Negrotto L, Farez M, Hohlfeld R, Pröbstel AK, Jia X, Graves J, Bar-or A, Oksenberg JR, Gelfand J, Wilson MR, Crabtree E, Zamvil SS, Correale J, Cree BA, Hauser SL, Knight R, Baranzini SE. Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis. Mult Scler 2020; 27:1352458520924594. [PMID: 33115343 PMCID: PMC7968892 DOI: 10.1177/1352458520924594] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Evidence for a role of human gut microbiota in multiple sclerosis (MS) risk is mounting, yet large variability is seen across studies. This is, in part, due to the lack of standardization of study protocols, sample collection methods, and sequencing approaches. OBJECTIVE This study aims to address the effect of a household experimental design, sample collection, and sequencing approaches in a gut microbiome study in MS subjects from a multi-city study population. METHODS We analyzed 128 MS patient and cohabiting healthy control pairs from the International MS Microbiome Study (iMSMS). A total of 1005 snap-frozen or desiccated Q-tip stool samples were collected and evaluated using 16S and shallow whole-metagenome shotgun sequencing. RESULTS The intra-individual variance observed by different collection strategies was dramatically lower than inter-individual variance. Shallow shotgun highly correlated with 16S sequencing. Participant house and recruitment site accounted for the two largest sources of microbial variance, while higher microbial similarity was seen in household-matched participants as hypothesized. A significant proportion of the variance in dietary intake was also dominated by geographic distance. CONCLUSION A household pair study largely overcomes common inherent limitations and increases statistical power in population-based microbiome studies.
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21
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Ordiz MI, Janssen S, Humphrey G, Ackermann G, Stephenson K, Agapova S, Divala O, Kaimila Y, Maleta K, Zhong C, Knight R, Trehan I, Tarr PI, Rusconi B, Manary MJ. The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months. Am J Clin Nutr 2020; 111:884-892. [PMID: 32047925 PMCID: PMC8287943 DOI: 10.1093/ajcn/nqaa011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Common bean and cowpea contain about 25% protein and 25% fiber, and are recommended as complementary foods in sub-Saharan Africa. OBJECTIVE The objective of this study was to determine if a daily legume supplement given to Malawian infants aged 6 to 12 mo alters the 16S configuration of the fecal microbiota as read out by amplicon sequence variants (ASVs). METHODS This study was conducted within the context of a randomized, double-blind, controlled clinical trial to assess whether cowpea or common bean supplementation reduced intestinal permeability or increased linear growth. There were 2 village clusters in which the study was conducted. Fresh stool collections were flash frozen from 236 infants at ≤6 time points. The stools were sequenced using Earth Microbiome project protocols and data were processed using Qiime and Qiita, open-source, validated software packages. α-diversity was measured using the Faith's test. The 16S configuration was characterized by determining the weighted UniFrac distances of the ASVs and comparing them using permutational multivariate ANOVA. RESULTS Among the 1249 samples analyzed, the α-diversity of the fecal microbiome was unchanged among subjects after initiation of legume supplementation. Neither cowpea nor common bean altered the overall 16S configuration at any age. The 16S configuration differed between children with adequate and poor linear growth aged from 6 to 9 mo, but no specific ASVs differed in relative abundance. The 16S configuration differed between children with normal and abnormal intestinal permeability at 9 mo, but no specific ASVs differed in relative abundance. Among categorical characteristics of the population associated with different 16S configurations, village cluster was most pronounced. CONCLUSION Legume supplementation in breastfed, rural African infants did not affect the structure of the gut microbial communities until the children were aged 9 mo. This trial was registered at clinicaltrials.gov as NCT02472262.
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Affiliation(s)
- M Isabel Ordiz
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Kevin Stephenson
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Sophia Agapova
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Oscar Divala
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Yankho Kaimila
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Ken Maleta
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Caroline Zhong
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
- Department of Computer Science and Engineering, University of
California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego,
La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San
Diego, La Jolla, CA, USA
| | - Indi Trehan
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
- Department of Paediatrics and Child Health, University of Malawi,
Blantyre, Malawi
| | - Phillip I Tarr
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Brigida Rusconi
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Mark J Manary
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
- USDA/Agricultural Research Service Children's Nutrition Research
Center, Houston, TX, USA
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22
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Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems 2019; 4:e00375-19. [PMID: 31551401 PMCID: PMC6759567 DOI: 10.1128/msystems.00375-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023] Open
Abstract
To visualize the personalized distributions of pathogens and chemical environments, including microbial metabolites, pharmaceuticals, and their metabolic products, within and between human lungs afflicted with cystic fibrosis (CF), we generated three-dimensional (3D) microbiome and metabolome maps of six explanted lungs from three cystic fibrosis patients. These 3D spatial maps revealed that the chemical environments differ between patients and within the lungs of each patient. Although the microbial ecosystems of the patients were defined by the dominant pathogen, their chemical diversity was not. Additionally, the chemical diversity between locales in the lungs of the same individual sometimes exceeded interindividual variation. Thus, the chemistry and microbiome of the explanted lungs appear to be not only personalized but also regiospecific. Previously undescribed analogs of microbial quinolones and antibiotic metabolites were also detected. Furthermore, mapping the chemical and microbial distributions allowed visualization of microbial community interactions, such as increased production of quorum sensing quinolones in locations where Pseudomonas was in contact with Staphylococcus and Granulicatella, consistent with in vitro observations of bacteria isolated from these patients. Visualization of microbe-metabolite associations within a host organ in early-stage CF disease in animal models will help elucidate the complex interplay between the presence of a given microbial structure, antibiotics, metabolism of antibiotics, microbial virulence factors, and host responses.IMPORTANCE Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same pathogen and how community interactions shape the chemical environment or vice versa. We highlight that three-dimensional organ mapping methods represent hypothesis-building tools that allow us to design mechanistic studies aimed at addressing microbial responses to other microbes, the host, and pharmaceutical drugs.
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Affiliation(s)
- Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California, San Diego, La Jolla, California, USA
- UC San Diego Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Embriette Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mingxun Wang
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Ivan Protsyuk
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jason V Wu
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yan Wei Lim
- Biology Department, San Diego State University, San Diego, California, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - William Comstock
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Robert A Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Richard Wong
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Timothy Spivey
- Department of Radiology, University of California, San Diego, La Jolla, California, USA
| | - Sharon S Brouha
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Nuno Bandeira
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
| | - Grace Y Lin
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Forest Rohwer
- Biology Department, San Diego State University, San Diego, California, USA
| | - Douglas J Conrad
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
- UC San Diego Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Center for Cystic Fibrosis and Airways Disease Research, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
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23
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Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC. The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biol 2019; 17:47. [PMID: 31189482 PMCID: PMC6560912 DOI: 10.1186/s12915-019-0660-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/30/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a moisturizer, a foot powder, and a deodorant) on 11 volunteers over 9 weeks. RESULTS Mass spectrometry and 16S rRNA inventories of the skin revealed decreases in chemical as well as in bacterial and archaeal diversity on halting deodorant use. Specific compounds from beauty products used before the study remain detectable with half-lives of 0.5-1.9 weeks. The deodorant and foot powder increased molecular, bacterial, and archaeal diversity, while arm and face lotions had little effect on bacterial and archaeal but increased chemical diversity. Personal care product effects last for weeks and produce highly individualized responses, including alterations in steroid and pheromone levels and in bacterial and archaeal ecosystem structure and dynamics. CONCLUSIONS These findings may lead to next-generation precision beauty products and therapies for skin disorders.
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Affiliation(s)
- Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Ricardo da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
- Department for Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Chris Callewaert
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
- Center for Microbial Ecology and Technology, Ghent University, 9000, Ghent, Belgium
| | - Amnon Amir
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Livia S Zaramela
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Ji-Nu Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92307, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92307, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92307, USA.
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92037, USA.
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24
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Brunt VE, Gioscia‐Ryan RA, Richey JJ, Zigler MC, Cuevas LM, Gonzalez A, Vázquez‐Baeza Y, Battson ML, Smithson AT, Gilley AD, Ackermann G, Neilson AP, Weir T, Davy KP, Knight R, Seals DR. Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice. J Physiol 2019; 597:2361-2378. [PMID: 30714619 PMCID: PMC6487935 DOI: 10.1113/jp277336] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/23/2019] [Indexed: 12/21/2022] Open
Abstract
KEY POINTS Age-related arterial dysfunction, characterized by oxidative stress- and inflammation-mediated endothelial dysfunction and arterial stiffening, is the primary risk factor for cardiovascular diseases. To investigate whether age-related changes in the gut microbiome may mediate arterial dysfunction, we suppressed gut microbiota in young and old mice with a cocktail of broad-spectrum, poorly-absorbed antibiotics in drinking water for 3-4 weeks. In old mice, antibiotic treatment reversed endothelial dysfunction and arterial stiffening and attenuated vascular oxidative stress and inflammation. To provide insight into age-related changes in gut microbiota that may underlie these observations, we show that ageing altered the abundance of microbial taxa associated with gut dysbiosis and increased plasma levels of the adverse gut-derived metabolite trimethylamine N-oxide. The results of the present study provide the first proof-of-concept evidence that the gut microbiome is an important mediator of age-related arterial dysfunction and therefore may be a promising therapeutic target for preserving arterial function with ageing, thereby reducing the risk of cardiovascular diseases. ABSTRACT Oxidative stress-mediated arterial dysfunction (e.g. endothelial dysfunction and large elastic artery stiffening) is the primary mechanism driving age-related cardiovascular diseases. Accumulating evidence suggests the gut microbiome modulates host physiology because dysregulation ('gut dysbiosis') has systemic consequences, including promotion of oxidative stress. The present study aimed to determine whether the gut microbiome modulates arterial function with ageing. We measured arterial function in young and older mice after 3-4 weeks of treatment with broad-spectrum, poorly-absorbed antibiotics to suppress the gut microbiome. To identify potential mechanistic links between the gut microbiome and age-related arterial dysfunction, we sequenced microbiota from young and older mice and measured plasma levels of the adverse gut-derived metabolite trimethylamine N-oxide (TMAO). In old mice, antibiotics reversed endothelial dysfunction [area-under-the-curve carotid artery dilatation to acetylcholine in young: 345 ± 16 AU vs. old control (OC): 220 ± 34 AU, P < 0.01; vs. old antibiotic-treated (OA): 334 ± 15 AU; P < 0.01 vs. OC] and arterial stiffening (aortic pulse wave velocity in young: 3.62 ± 0.15 m s-1 vs. OC: 4.43 ± 0.38 m s-1 ; vs. OA: 3.52 ± 0.35 m s-1 ; P = 0.03). These improvements were accompanied by lower oxidative stress and greater antioxidant enzyme expression. Ageing altered the abundance of gut microbial taxa associated with gut dysbiosis. Lastly, plasma TMAO was higher with ageing (young: 2.6 ± 0.4 μmol L-1 vs. OC: 7.2 ± 2.0 μmol L-1 ; P < 0.0001) and suppressed by antibiotic treatment (OA: 1.2 ± 0.2 μmol L-1 ; P < 0.0001 vs. OC). The results of the present study provide the first evidence for the gut microbiome being an important mediator of age-related arterial dysfunction and oxidative stress and suggest that therapeutic strategies targeting gut microbiome health may hold promise for preserving arterial function and reducing cardiovascular risk with ageing in humans.
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Affiliation(s)
- Vienna E. Brunt
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
| | | | - James J. Richey
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
| | - Melanie C. Zigler
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
| | - Lauren M. Cuevas
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
| | - Antonio Gonzalez
- Department of PediatricsUniversity of California San DiegoLa JollaCAUSA
| | | | - Micah L. Battson
- Department of Food Science & Human NutritionColorado State UniversityFort CollinsCOUSA
| | - Andrew T. Smithson
- Department of Food Science and TechnologyVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Andrew D. Gilley
- Department of Food Science and TechnologyVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Gail Ackermann
- Department of PediatricsUniversity of California San DiegoLa JollaCAUSA
| | - Andrew P. Neilson
- Department of Food Science and TechnologyVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Tiffany Weir
- Department of Food Science & Human NutritionColorado State UniversityFort CollinsCOUSA
| | - Kevin P. Davy
- Department of Human Nutrition, Foods, and ExerciseVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Rob Knight
- Department of PediatricsUniversity of California San DiegoLa JollaCAUSA
- Department of Computer Science and EngineeringUniversity of California San DiegoLa JollaCAUSA
- Center for Microbiome InnovationUniversity of California San DiegoLa JollaCAUSA
| | - Douglas R. Seals
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
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25
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Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O’Donoghue AJ, Knight R, Dorrestein PC. Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome. Microbiome 2019; 7:23. [PMID: 30760325 PMCID: PMC6375204 DOI: 10.1186/s40168-019-0636-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/29/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However, how this phenomenon is reflected in the metabolites and chemical environment of lung secretions remains poorly understood. METHODS Here we investigated the microbial and molecular composition of CF sputum samples using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry to determine their interrelationships and associations with clinical measures of disease severity. RESULTS The CF metabolome was found to exist in two states: one from patients with more severe disease that had higher molecular diversity and more Pseudomonas aeruginosa and the other from patients with better lung function having lower metabolite diversity and fewer pathogenic bacteria. The two molecular states were differentiated by the abundance and diversity of peptides and amino acids. Patients with severe disease and more pathogenic bacteria had higher levels of peptides. Analysis of the carboxyl terminal residues of these peptides indicated that neutrophil elastase and cathepsin G were responsible for their generation, and accordingly, these patients had higher levels of proteolytic activity from these enzymes in their sputum. The CF pathogen Pseudomonas aeruginosa was correlated with the abundance of amino acids and is known to primarily feed on them in the lung. CONCLUSIONS In cases of severe CF lung disease, proteolysis by host enzymes creates an amino acid-rich environment that P. aeruginosa comes to dominate, which may contribute to the pathogen's persistence by providing its preferred carbon source.
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Affiliation(s)
- Robert A. Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48823 MI USA
| | - Sandeep Adem
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Robert H. Mills
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
| | - William Comstock
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | | | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
| | - Alexander A. Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Alexei V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Ricardo da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
| | - David J. Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA USA
| | - Doug Conrad
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
- Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
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26
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Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods 2018; 15:796-798. [PMID: 30275573 PMCID: PMC6235622 DOI: 10.1038/s41592-018-0141-9] [Citation(s) in RCA: 338] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
Abstract
Multi-omic insights into microbiome function and composition typically advance one study at a time. However, to understand relationships across studies, they must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome comparison platform, which we demonstrate with Human Microbiome Project and iHMP data.
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Affiliation(s)
- Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.,Google LLC, Mountain View, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jeff DeReus
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Janssen
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie B Orchanian
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Shorenstein
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Inscripta, Inc., Boulder, CO, USA
| | - Hannes Holste
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Semar Petrus
- Department of Biology, University of California, San Diego, La Jolla, CA, USA
| | - Adam Robbins-Pianka
- Department of Computer Science, University of Colorado, Boulder, Boulder, CO, USA
| | - Colin J Brislawn
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jai Ram Rideout
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Evan Bolyen
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Matthew Dillon
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
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27
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Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Sci Adv 2018; 4:eaau1908. [PMID: 30263961 PMCID: PMC6157970 DOI: 10.1126/sciadv.aau1908] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/10/2018] [Indexed: 05/25/2023]
Abstract
Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communities in the human body from undesirable dysbiotic states.
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Affiliation(s)
- Robert A. Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
| | - William Comstock
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tianyu Zhang
- Department of Mathematical Sciences, Montana State University, Bozeman, MT 59717, USA
| | - James T. Morton
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ricardo da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alda Tran
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexander Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
| | - Louis-Felix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Daniel Wangpraseurt
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexey V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Douglas Conrad
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Isaac Klapper
- Department of Mathematics, Temple University, Philadelphia, PA 19122, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA
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28
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Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 2017; 551:457-463. [PMID: 29088705 PMCID: PMC6192678 DOI: 10.1038/nature24621] [Citation(s) in RCA: 1219] [Impact Index Per Article: 174.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Joshua Ladau
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kenneth J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert J Prill
- Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
| | - Mohamed F Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jad Kanbar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joshua Lefler
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Donna Berg-Lyons
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.,Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Katherine S Pollard
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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29
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Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe 2017; 22:705-716.e4. [PMID: 29056429 DOI: 10.1016/j.chom.2017.10.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/12/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022]
Abstract
Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and region-specific metabolism of medications and placed it in the context of microbial distributions in the lung. Our tool further created browsable maps of a 3D microbiome/metabolome reconstruction map on a radiological image of a human lung and forms an interactive resource for the scientific community.
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Affiliation(s)
- Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Embriette Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Protsyuk
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yan Wei Lim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Richard Wong
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Timothy Spivey
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Sharon S Brouha
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Nuno Bandeira
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace Y Lin
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Forest Rohwer
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Douglas J Conrad
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Rob Knight
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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30
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Potter C, Freeman C, Golyshin PN, Ackermann G, Fenner N, McDonald JE, Ehbair A, Jones TG, Murphy LM, Creer S. Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems. Sci Rep 2017; 7:11314. [PMID: 28900257 PMCID: PMC5595961 DOI: 10.1038/s41598-017-11546-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/10/2017] [Indexed: 12/01/2022] Open
Abstract
Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat ‘mesocosm cores’ taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. ‘Drought-responsive’ OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.
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Affiliation(s)
- Caitlin Potter
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK
| | - Chris Freeman
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK
| | - Gail Ackermann
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, USA
| | - Nathalie Fenner
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK
| | - James E McDonald
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK
| | - Abdassalam Ehbair
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK.,School of Chemistry, Bangor University, Gwynedd, Wales, UK
| | - Timothy G Jones
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK
| | | | - Simon Creer
- School of Biological Sciences, Bangor University, Gwynedd, Wales, UK.
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31
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Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. eLife 2017; 6. [PMID: 28492366 PMCID: PMC5441867 DOI: 10.7554/elife.24214] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium. DOI:http://dx.doi.org/10.7554/eLife.24214.001 Cyanobacteria and algae are found in all oceans around the globe. Like plants, they can use sunlight as a source of energy in a process called photosynthesis. As a result, these organisms are important sources of oxygen and another vital nutrient called nitrogen for other marine organisms. Many of these organisms also produce a variety of other chemicals known as “natural products” to help them to survive in their environments. Some of these natural products have shown potential as medicinal drugs. The search for new chemicals with useful medicinal properties has led researchers to collect samples of algae and cyanobacteria from various locations around the world. An approach called mass spectrometry is often used to identify new chemicals because it can provide information about the structure of a molecule based on how much its fragments weigh. Luzzatto-Knaan et al. used mass spectrometry to search for new chemicals in samples of algae and cyanobacteria that had been collected by diving and snorkeling in a wide variety of tropical marine environments over several decades. The experiments reveal that the organisms in these samples produce a diverse range of chemicals, most of which were previously unknown and have not been found in other similar environmental collections. The data were grouped together into eight major collection areas covering different parts of the tropics. The samples from some areas contained a wider variety of chemicals than others. Within each collection area, some molecules were found to be very common whereas others were only present at specific locations. To highlight the distribution of these natural products, Luzzatto-Knaan et al. display the data on a world map. Further experiments used this approach as a guide to extract a previously unknown chemical called yuvalamide A from a marine cyanobacterium. The next challenge would be to associate the geographical patterns of chemicals to their potential ecological roles. This approach offers a new way to explore large-scale collections of environmental samples to discover and study new natural products. DOI:http://dx.doi.org/10.7554/eLife.24214.002
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Mingxun Wang
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, United States
| | - Gail Ackermann
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Amnon Amir
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
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32
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Scanlan PD, Knight R, Song SJ, Ackermann G, Cotter PD. Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infect Genet Evol 2016; 45:95-97. [PMID: 27545648 DOI: 10.1016/j.meegid.2016.08.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/04/2016] [Accepted: 08/17/2016] [Indexed: 02/08/2023]
Abstract
The human gut is host to a diversity of microorganisms including the single-celled microbial eukaryote Blastocystis. Although Blastocystis has a global distribution, there is dearth of information relating to its prevalence and diversity in many human populations. The mode of Blastocystis transmission to humans is also insufficiently characterised, however, it is speculated to vary between different populations. Here we investigated the incidence and genetic diversity of Blastocystis in a US population and also the possibility of Blastocystis human-human transmission between healthy individuals using family units (N=50) living in Boulder, Colorado as our sample-set. Ten of the 139 (~7%) individuals in our dataset were positive for Blastocystis, nine of whom were adults and one individual belonging to the children/adolescents group. All positive cases were present in different family units. A number of different Blastocystis subtypes (species) were detected with no evidence of mixed infections. The prevalence of Blastocystis in this subset of the US population is comparatively low relative to other industrialised populations investigated to date; however, subtype diversity was largely consistent with that previously reported in studies of European populations. The distribution of Blastocystis within family units indicates that human-human transmission is unlikely to have occurred within families that participated in this study. It is not unexpected that given the world-wide variation in human living conditions and lifestyles between different populations, both the prevalence of Blastocystis and its mode of transmission to humans may vary considerably.
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Affiliation(s)
- Pauline D Scanlan
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; APC Microbiome Institute, Biosciences Institute, University College Cork, Cork, Ireland.
| | - Rob Knight
- Department of Pediatrics and Computer Science & Engineering, University of California at San Diego, San Diego, CA, USA
| | - Se Jin Song
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics and Computer Science & Engineering, University of California at San Diego, San Diego, CA, USA
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; APC Microbiome Institute, Biosciences Institute, University College Cork, Cork, Ireland
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Amato KR, Metcalf JL, Song SJ, Hale VL, Clayton J, Ackermann G, Humphrey G, Niu K, Cui D, Zhao H, Schrenzel MD, Tan CL, Knight R, Braun J. Using the gut microbiota as a novel tool for examining colobine primate GI health. Glob Ecol Conserv 2016. [DOI: 10.1016/j.gecco.2016.06.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG. Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets. Gigascience 2016; 5:27. [PMID: 27296526 PMCID: PMC4906574 DOI: 10.1186/s13742-016-0133-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. MAIN TEXT We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. CONCLUSIONS Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.
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Affiliation(s)
- Jai Ram Rideout
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - John H Chase
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Evan Bolyen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, 92093, USA
| | - J Gregory Caporaso
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
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Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 2015; 351:158-62. [PMID: 26657285 DOI: 10.1126/science.aad2646] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022]
Abstract
Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.
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Affiliation(s)
- Jessica L Metcalf
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Simon Lax
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL 606037, USA
| | - Will Van Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Embriette R Hyde
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Se Jin Song
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Amnon Amir
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Peter Larsen
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA
| | - Naseer Sangwan
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA. Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Daniel Haarmann
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Greg C Humphrey
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Luke R Thompson
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Christian Lauber
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale Lausanne, Bâtiment H, 1015 Lausanne, Switzerland
| | - Alexander Bibat
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | | | - Matthew J Gebert
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT 84532, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL 606037, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA. Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA. Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA
| | - Aaron M Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Sibyl R Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA. Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92037, USA.
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Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S, McHardy A, Dangl J, Knight R, Ley R, Schulze-Lefert P. Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host Microbe 2015; 17:603-16. [DOI: 10.1016/j.chom.2015.04.009] [Citation(s) in RCA: 439] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Lin P, Bach M, Asquith M, Lee AY, Akileswaran L, Stauffer P, Davin S, Pan Y, Cambronne ED, Dorris M, Debelius JW, Lauber CL, Ackermann G, Baeza YV, Gill T, Knight R, Colbert RA, Taurog JD, Van Gelder RN, Rosenbaum JT. HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats. PLoS One 2014; 9:e105684. [PMID: 25140823 PMCID: PMC4139385 DOI: 10.1371/journal.pone.0105684] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
The HLA-B27 gene is a major risk factor for clinical diseases including ankylosing spondylitis, acute anterior uveitis, reactive arthritis, and psoriatic arthritis, but its mechanism of risk enhancement is not completely understood. The gut microbiome has recently been shown to influence several HLA-linked diseases. However, the role of HLA-B27 in shaping the gut microbiome has not been previously investigated. In this study, we characterize the differences in the gut microbiota mediated by the presence of the HLA-B27 gene. We identified differences in the cecal microbiota of Lewis rats transgenic for HLA-B27 and human β2-microglobulin (hβ2m), compared with wild-type Lewis rats, using biome representational in situ karyotyping (BRISK) and 16S rRNA gene sequencing. 16S sequencing revealed significant differences between transgenic animals and wild type animals by principal coordinates analysis. Further analysis of the data set revealed an increase in Prevotella spp. and a decrease in Rikenellaceae relative abundance in the transgenic animals compared to the wild type animals. By BRISK analysis, species-specific differences included an increase in Bacteroides vulgatus abundance in HLA-B27/hβ2m and hβ2m compared to wild type rats. The finding that HLA-B27 is associated with altered cecal microbiota has not been shown before and can potentially provide a better understanding of the clinical diseases associated with this gene.
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Affiliation(s)
- Phoebe Lin
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
| | - Mary Bach
- Division of Rheumatology, University of Washington, VA Medical Center, Seattle, Washington, United States of America
| | - Mark Asquith
- Division of Rheumatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Aaron Y. Lee
- Moorfield's Eye Institute of London, London, United Kingdom
| | - Lakshmi Akileswaran
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States of America
| | - Patrick Stauffer
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Sean Davin
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Yuzhen Pan
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Eric D. Cambronne
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Martha Dorris
- Department of Rheumatology, University of Texas Southwestern, Dallas, Texas, United States of America
| | | | | | - Gail Ackermann
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Yoshiki V. Baeza
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Tejpal Gill
- Pediatric Translational Research Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Rob Knight
- University of Colorado Boulder, Boulder, Colorado, United States of America
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Robert A. Colbert
- Pediatric Translational Research Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Joel D. Taurog
- Department of Rheumatology, University of Texas Southwestern, Dallas, Texas, United States of America
| | - Russell N. Van Gelder
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States of America
| | - James T. Rosenbaum
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Rheumatology, Oregon Health & Science University, Portland, Oregon, United States of America
- Dever's Eye Institute, Portland, Oregon, United States of America
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Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2013; 2:e01104. [PMID: 24137541 PMCID: PMC3796315 DOI: 10.7554/elife.01104] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/20/2013] [Indexed: 12/13/2022] Open
Abstract
Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI:http://dx.doi.org/10.7554/eLife.01104.001 Our bodies—especially our skin, our saliva, the lining of our mouth and our gastrointestinal tract—are home to a diverse collection of bacteria and other microorganisms called the microbiome. While the roles played by many of these microorganisms have yet to be identified, it is known that they contribute to the health and wellbeing of their host by metabolizing indigestible compounds, producing essential vitamins, and preventing the growth of harmful bacteria. They are important for nutrient and carbon cycling in the environment. The advent of advanced sequencing techniques has made it feasible to study the composition of this microbial community, and to monitor how it changes over time or how it responds to events such as antibiotic treatment. Sequencing studies have been used to highlight the significant differences between microbial communities found in different parts of the body, and to follow the evolution of the gut microbiome from birth. Most of these studies have focused on live animals, so little is known about what happens to the microbiome after its host dies. In particular, it is not known if the changes that occur after death are similar for all individuals. Moreover, the decomposing animal supplies nutrients and carbon to the surrounding ecosystem, but its influence on the microbial community of its immediate environment is not well understood. Now Metcalf et al. have used high-throughput sequencing to study the bacteria and other microorganisms (such as nematodes and fungi) in dead and decomposing mice, and also in the soil beneath them, over the course of 48 days. The changes were significant and also consistent across the corpses, with the microbial communities in the corpses influencing those in the soil, and vice versa. Metcalf et al. also showed that these measurements could be used to estimate the postmortem interval (the time since death) to within approximately 3 days, which suggests that the work could have applications in forensic science. DOI:http://dx.doi.org/10.7554/eLife.01104.002
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Affiliation(s)
- Jessica L Metcalf
- Biofrontiers Institute , University of Colorado at Boulder , Boulder , United States
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Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R. Meta-analyses of studies of the human microbiota. Genome Res 2013; 23:1704-14. [PMID: 23861384 PMCID: PMC3787266 DOI: 10.1101/gr.151803.112] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ileal Crohn's disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.
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Affiliation(s)
- Catherine A Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
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Reuse K, Ackermann G, Busch C, Schütte W. Der T-Spot-Tb in der bronchoalveolären Lavage im Vergleich zum Blut. Pneumologie 2011. [DOI: 10.1055/s-0031-1297382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Ilchmann C, Zaiß NH, Speicher A, Christner M, Ackermann G, Rohde H. Comparison of resistance against erythromycin and moxifloxacin, presence of binary toxin gene and PCR ribotypes in Clostridium difficile isolates from 1990 and 2008. Eur J Clin Microbiol Infect Dis 2010; 29:1571-3. [DOI: 10.1007/s10096-010-1017-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 06/25/2010] [Indexed: 01/05/2023]
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Breskot T, Skrzipek H, Eichler J, Schulz HJ, Ackermann G, Sander B, Frie B, Schneeweiß-Wolter C. Hologrammsynthese von MRT-Schichtbildern. BIOMED ENG-BIOMED TE 2009. [DOI: 10.1515/bmte.1995.40.s1.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Spencer B, Broesskamp-Stone U, Ruckstuhl B, Ackermann G, Spoerri A, Cloetta B. Modelling the results of health promotion activities in Switzerland: development of the Swiss Model for Outcome Classification in Health Promotion and Prevention. Health Promot Int 2008; 23:86-97. [DOI: 10.1093/heapro/dam038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Zaiss NH, Weile J, Ackermann G, Kuijper E, Witte W, Nüebel U. A case of Clostridium difficile-associated disease due to the highly virulent clone of Clostridium difficile PCR ribotype 027, March 2007 in Germany. ACTA ACUST UNITED AC 2007; 12:E071115.1. [PMID: 18005641 DOI: 10.2807/esw.12.46.03306-en] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the isolation of C. difficile PCR ribotype 027 from a patient suffering from pseudomembranous colitis in Germany in March 2007. The strain was identified during a retrospective PCR ribotyping survey of stored isolates.
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Affiliation(s)
- N H Zaiss
- Robert Koch Institute, Wernigerode, Germany
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Flemming K, Ackermann G. Prevalence of Enterotoxin Producing Staphylococcus aureus in Stools of Patients with Nosocomial Diarrhea. Infection 2007; 35:356-8. [PMID: 17721737 DOI: 10.1007/s15010-007-6268-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 05/03/2007] [Indexed: 11/26/2022]
Abstract
BACKGROUND Nosocomial diarrhea causes prolonged hospital stay leading to additional diagnostic and therapeutic procedures resulting in higher costs. A total of 20%-25% of antibiotic-associated diarrhea (AAD) cases are attributed to Clostridium difficile. Other microorganisms like Clostridium perfringens and Staphylococcus aureus are discussed to be associated with AAD. PATIENTS AND METHODS This study evaluated the prevalence of enterotoxigenic S. aureus in stool samples submitted to the laboratory with the diagnosis nosocomial diarrhea. A total of 2,727 stools from clinical patients were investigated for S. aureus and C. difficile. Samples were cultured for both bacteria and a C. difficile toxin A and B assay was performed from all stools. Isolated S. aureus were investigated for enterotoxin production and for resistance against methicillin. In addition, both assays were evaluated for determination of S. aureus enterotoxins directly in stool samples. RESULTS Out of 2,727 stools investigated, 198 grew S. aureus and 148 C. difficile. Toxins A/B from C. difficile were detected in 184 stools. A total of 114 S. aureus strains produced the following enterotoxins in vitro: A, 36; B, 20; C, 19; D, 68; E, 2. Both pathogens were found in 25 stools. Twenty-nine (14.6%) S. aureus strains were identified as methicillin-resistant. The two toxin assays evaluated in this study were not able to detect S. aureus enterotoxins directly in stools. CONCLUSION The role of enterotoxigenic S. aureus in the pathogenesis of nosocomial and AAD needs further consideration. It might be necessary to investigate stool samples from patients with AAD/nosocomial diarrhea for S. aureus on a routine basis.
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Affiliation(s)
- K Flemming
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University of Leipzig, 04103, Leipzig, Germany
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Ackermann G, Löffler B, Tang-Feldman YJ, Cohen SH, Silva J, Rodloff AC. Cloning and expression of Clostridium difficile toxin A gene (tcdA) by PCR amplification and use of an expression vector. Mol Cell Probes 2004; 18:271-4. [PMID: 15271388 DOI: 10.1016/j.mcp.2004.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 02/20/2004] [Indexed: 11/16/2022]
Abstract
Toxigenic Clostridium difficile isolates harbor a 19 kb pathogenicity locus that encodes the genes for toxins A and B. Toxins A and B are among the largest known bacterial toxins expressing potent cytotoxicity and enterotoxicity, and thus the major virulence factors in C. difficile associated diarrhea. Cloning and sequencing of toxin genes is of interest for studies of molecular pathogenesis. We report the amplification and cloning of the complete toxin A gene into an Escherichia coli expression vector. Ten clones analyzed contained the complete toxin A gene. Four of these clones showed cytotoxic activity in cell culture, and were positive for toxin A as determined by ELISA. Toxin A expression was confirmed by Western immunoblot analysis. The presence of cytotoxic activity in cell culture suggests that toxin A activity is independent of other genes in the pathogenicity locus.
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Affiliation(s)
- G Ackermann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University of Leipzig, Liebigstrasse 24, 04103 Leipzig, Germany.
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Scherer K, Abels C, Bäumler W, Ackermann G, Szeimies RM. Structure-activity relationships of three differently substituted 2,7,12,17-tetrakis-(�-methoxyethyl) porphycene derivatives in vitro. Arch Dermatol Res 2004; 295:535-41. [PMID: 15034722 DOI: 10.1007/s00403-004-0458-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2003] [Revised: 01/26/2004] [Accepted: 02/01/2004] [Indexed: 11/26/2022]
Abstract
The subcellular localization, efficacy and photooxidative mechanism of three new photosensitizing porphycenes (HexoTMPn, PeloTMPn, CpoTMPn) for photodynamic therapy with different substituents at position 9 of the tetrapyrrole macrocycle were investigated in vitro using different human skin-derived cell lines (HaCaT, SCL I, SCL II) with the aim of customizing the side-chain chemistry to accelerate cellular uptake and so enhance photodynamic activity. Cells were incubated with a porphycene and costained with organelle-specific markers. Subcellular localization was determined by fluorescence microscopy. Also, cells were incubated with different sensitizer concentrations (0-1000 nmol/l) and irradiated by an incoherent light source (lambda(em) = 600-750 nm, 40 mW/cm(2), 24 J/cm(2)) with/without quenchers or enhancers (NaN(3), histidine, mannitol or D(2)O). Cell viability was assessed. All porphycenes were localized in perinuclear lysosomes and induced a decrease in mitochondrial activity following irradiation. HexoTMPn was the most efficient in all three cell lines (EC(50) in HaCaT cells: HexoTMPn 14 nmol/l, CpoTMPn 62 nmol/l, PeloTMPn 89 nmol/l). Addition of either NaN(3) or histidine reduced the phototoxicity significantly. Due to the short lifetime of singlet oxygen, the sites of sensitizer localization are the initial subcellular targets. The cytotoxicity of each sensitizer varied depending on singlet oxygen quantum yield and cell line. Despite the different chemical structures, the biological effects were not very distinct, since they seemed to be mostly determined by the tetrapyrrole ring and only slightly modified by the substituent at position 9. Also, there was only a narrow margin between biological compatibility and efficacy.
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Affiliation(s)
- Kathrin Scherer
- Department of Dermatology, University of Regensburg, 93042 Regensburg, Germany
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Ackermann G, Tang-Feldman YJ, Schaumann R, Henderson JP, Rodloff AC, Silva J, Cohen SH. Antecedent use of fluoroquinolones is associated with resistance to moxifloxacin in Clostridium difficile. Clin Microbiol Infect 2003; 9:526-30. [PMID: 12848728 DOI: 10.1046/j.1469-0691.2003.00559.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE Moxifloxacin is characterized by high activity against Gram-positive cocci and some Gram-positive and -negative anaerobes, including Clostridium difficile. This study investigates the role of prior quinolone use in relation to patterns of susceptibility of C. difficile to moxifloxacin. METHODS Sixty-three clinical isolates of C. difficile were investigated for toxigenicity, susceptibility to moxifloxacin, and mutations in the DNA gyrase gene. The medical histories for 50 of these patients were available and used to identify previous fluoroquinolone use. RESULTS Thirty-three (52.4%) strains showed resistance to moxifloxacin (MICs > or = 16 mg/L). All moxifloxacin-resistant strains harbored a mutation at amino acid codon Ser-83 of gyrA. Forty-five isolates (71.4%) were toxigenic; all moxifloxacin-resistant strains were in this group. Resistance to moxifloxacin was associated with prior use of fluoroquinolones (P-value 0.009, chi-square). CONCLUSIONS Although the use of moxifloxacin to treat C. difficile-associated diarrhea is not likely to be common, these data show a relationship between antecedent fluoroquinolone use and resistance to moxifloxacin in C. difficile isolates, and raise questions regarding selection pressure for resistance placed on colonizing bacteria exposed to fluoroquinolones. Mutations in gyrA are involved in moxifloxacin resistance.
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Affiliation(s)
- G Ackermann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University of Leipzig, Leipzig, Germany.
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Ackermann G, Hartmann M, Scherer K, Lang EW, Hohenleutner U, Landthaler M, Bäumler W. Correlations between light penetration into skin and the therapeutic outcome following laser therapy of port-wine stains. Lasers Med Sci 2002; 17:70-8. [PMID: 12111589 DOI: 10.1007/s101030200013] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
For several years the flashlamp-pumped pulsed dye laser (FPDL) has been the favoured method for the treatment of port-wine stains (PWS). The therapeutic outcome of FPDL laser therapy depends on the anatomical location of the PWS and is mainly attributed to morphological parameters such as size and depth of the PWS blood vessels. The aim of this study was to show a correlation between the therapeutic outcome following FPDL therapy and the optical properties of the skin overlying the PWS vessels. For this purpose the therapeutic outcome following FPDL treatment (585 nm; 0.45 ms) of 884 PWS situated on different body sites was evaluated by judging the grade of fading of PWS colour. On the other hand the light penetration into 123 skin samples (thickness 0.10-1.35 mm) was determined between 450 nm and 1030 nm and compared with the PWS laser therapy outcome for equal locations by statistical analysis. PWS on the neck, trunk, arms or legs yielded a higher mean grade of fading as compared to PWS on the head. Within the face, a wide range of fading was evident. The light penetration into skin increased linearly with increasing wavelength and location-dependent differences were found. The attenuation coefficient was 22.8+/-5.3 mm(-1) at 585 nm. No significant or strong correlation was observed between the therapeutic outcome of PWS laser therapy and the light penetration into skin. However, a correlation was obvious by plotting the respective profile plots. Therefore, among other effects, in particular morphological parameters of PWS vessels, the optical properties of the skin contribute to a small extent to the clinical outcome of PWS laser therapy.
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Affiliation(s)
- G Ackermann
- Department of Dermatology, University of Regensburg, Germany
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Schaumann R, Sommer K, Retzlaff C, Ackermann G, Rodloff AC. Effects of Porphyromonas gingivalis on the activation of mouse macrophages by lipopolysaccharide. Eur J Med Res 2002; 7:447-52. [PMID: 12435623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
Porphyromonas gingivalis (PG) is a micro-organism that is suggested to play an etiologic role in acute and chronic periodontitis. The present study was undertaken to evaluate the question whether PG is capable of inducing interleukin (IL)-1beta, IL-6, macrophage inflammatory protein (MIP)-2, and granulocyte-macrophage colony-stimulating factor (GM-CSF) production in macrophages. Furthermore, the effect of PG on the activation of macrophages by Escherichia coli-lipopolysaccharide (LPS) was studied. The cytokines were analyzed by detection of specific mRNA. The mRNA was amplified by RT-PCR and semi-quantitatively analyzed by high performance liquid chromatography and densitometrically, respectively. These studies demonstrate that LPS was more active than PG in inducing mRNA expression of IL-1beta, IL-6, MIP-2 and GM-CSF. Moreover, PG reduced the mRNA expression of the macrophages stimulated with LPS, especially the IL-1beta and IL-6 mRNA expression was decreased.
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Affiliation(s)
- Reiner Schaumann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Leipzig, Liebigstr. 24, D-04103 Leipzig, Germany.
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